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VEGFA-derived hsa_circ_0076611 promotes proliferation by regulating translation initiation rate in triple-negative breast cancer

ABSTRACT: VEGFA-derived hsa_circ_0076611 promotes proliferation by regulating translation initiation rate in triple-negative breast cancer

PROVIDER: PRJNA762309 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15838448_1.fastq.gz	Fastqsanger.gz
	SRR15838448_2.fastq.gz	Fastqsanger.gz
	SRR15838449_1.fastq.gz	Fastqsanger.gz
	SRR15838449_2.fastq.gz	Fastqsanger.gz

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VEGFA-derived hsa_circ_0076611 promotes proliferation by regulating translation initiation rate in triple-negative breast cancer

Project description:Hsa_circ_0076611 is a circular RNA derived from back splicing of VEGFA exon 7 and expressed in triple-negative breast cancer (TNBC) cells and tissues. Through RNAseq analysis of hsa_circ_0076611-interacting RNAs, recovered by ChIRP assays, we here identified target mRNAs potentially controlled by hsa_circ_0076611 in MDA-MB-468 TNBC cells. Validation experiments confirmed that hsa_circ_0076611 interacts with and controls the expression of proliferation- and differentiation-related genes.

2022-06-08 | GSE183902 | GEO

Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide

Project description:The goal of this study is to evaluate the competition between eIF5 and 5MP in utilizing non-AUG translation initiation sites

2017-08-18 | GSE102786 | GEO

Synonymous codon usage regulates translation initiation

Project description:Synonymous codon usage regulates translation initiation

| PRJNA837608 | ENA

Protein translation rate determines neocortical neuron fate

Project description:Protein translation rate determines neocortical neuron fate

| PRJNA723552 | ENA

The eukaryotic translation initiation factor eIF4E regulates flowering and circadian rhythm in Arabidopsis

Project description:Translation initiation is a rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in the translation initiation process. However, how eIF4E-dependent translation initiation regulates plant growth and development remains not fully understood. In this study, we have found that Arabidopsis eIF4E proteins distribute both in the nucleus and cytoplasm, and only cytoplasmic eIF4E is implicated in the control of flowering time. Results of profiling the genome-wide translation by Ribo-tag sequencing further reveal that eIF4E may regulate plant flowering by affecting homeostatic translation of flowering-time genes, including the Central Oscillator Genes (COGs). Consistent with the hypothesis that transcription-translation feedback loop is the core mechanism to drive the oscillation of circadian clock, we show that the eIF4E-dependent translation modulates the rhythmic oscillation of protein abundance of the clock-related genes (CCGs). Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processed in Arabidopsis including circadian clock and photoperiodic flowering.

2023-10-25 | GSE245858 | GEO

Translation elongation rate varies among organs and decreases with age

Project description:There has been a surge of interest towards targeting protein synthesis to treat diseases and extend lifespan. Despite the progress, few options are available to assess translation in live animals, as their complexity limits the repertoire of experimental tools to monitor and manipulate processes within organs and individual cells. It this study, we developed a labeling-free method for measuring organ- and cell-type-specific translation elongation rates in vivo. It is based on time-resolved delivery of translation initiation and elongation inhibitors in live animals followed by ribosome profiling. It also reports translation initiation sites in an organ-specific manner. Using this method, we found that the elongation rates differ more than 50% among mouse organs and determined them to be 6.8, 5.0, and 4.3 amino acids per second for liver, kidney, and skeletal muscle, respectively. We further found that the elongation rate is reduced by 20% between young adulthood and mid-life. Thus, translation, a major metabolic process in cells, is tightly regulated at the level of elongation of nascent polypeptide chains.

2018-12-31 | GSE112223 | GEO

Deep sequencing reveals mRNA recruitment in translation initiation

Project description:We studied the initiation signals located in the translational initiation region (TIR) and identified the role for recognition of the initiation signals in each individual stage during formation of the initiation complexes. Sequencing the randomized mRNA libraries captured by translation initiation complexes

2016-07-27 | E-GEOD-69782 | biostudies-arrayexpress

Translation initiation landscape of tomato-infecting virus

Project description:Translation initiation landscape of tomato-infecting virus

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Synonymous codon usage regulates translation initiation

Project description:Ribo-seq with firefly luciferase optimality reporters to determine whether incomplete translation and/or inhibited translation initiation is responsible for the reduced ribosome occupancy on nonoptimal transcripts.

2022-05-16 | GSE202900 | GEO

A Chemical Kinetic Basis for Measuring Translation Initiation and Elongation Rates from Ribosome Profiling data

Project description:Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions; hence, bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. Applying our methods to data from S. cerevisiae and mouse embryonic stem cells we find that the extracted rates reproduce previously reported correlations with various molecular quantities. A codon can exhibit up to 26-fold variability in its translation rate depending upon its context with in a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated. We also find that mouse embryonic stem cells have a global translation speed that is almost two-fold faster than previously reported. This large variability in translation rates suggests that translational regulation might be used by cells to a greater degree than previously thought.

2018-08-07 | GSE116523 | GEO

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